parus: Parus major population dynamics

In kidusasfaw/pomp: Statistical Inference for Partially Observed Markov Processes

Description

Size of a population of great tits (Parus major) from Wytham Wood, near Oxford.

Details

Provenance: Global Population Dynamics Database dataset #10163. (NERC Centre for Population Biology, Imperial College (2010) The Global Population Dynamics Database Version 2. http://www.sw.ic.ac.uk/cpb/cpb/gpdd.html).

Original source: McCleer and Perrins (1991).

References

McCleery, R. & Perrins, C. (1991) Effects of predation on the numbers of Great Tits, Parus major. In: Bird Population Studies, edited by Perrins, C.M., Lebreton, J.-D. & Hirons, G.J.M. Oxford. Univ. Press. pp. 129–147.

See Also

Other datasets: blowflies, bsflu, dacca, measles

Examples

library(magrittr)

parus %>%
  pfilter(Np=1000,times="year",t0=1960,
  params=c(K=190,r=2.7,sigma=0.2,theta=0.05,N.0=148),
  rprocess=discrete_time(
     function (r, K, sigma, N, ...) {
       e <- rnorm(n=1,mean=0,sd=sigma)
       c(N = exp(log(N)+r*(1-N/K)+e))
     },
     delta.t=1
  ),
  rmeasure=function (N, theta, ...) {
     c(pop=rnbinom(n=1,size=1/theta,mu=N+1e-10))
  },
  dmeasure=function (pop, N, theta, ..., log) {
     dnbinom(x=pop,mu=N+1e-10,size=1/theta,log=log)
  },
  partrans=parameter_trans(log=c("sigma","theta","N_0","r","K")),
  paramnames=c("sigma","theta","N_0","r","K")
) -> pf

pf %>% logLik()

pf %>% simulate() %>% plot()

kidusasfaw/pomp documentation built on May 20, 2019, 2:59 p.m.